Sunday, 8 May 2011

MIOSS - Open Source in Chemistry workshop

I'm just back from the EBI where I participated in a Wellcome Trust workshop "Molecular Informatics Open Source Software", organised by Mark Forster of Syngenta. I gave a talk on Cinfony (slides to follow), while fellow Open Babel developers Tim Vandermeersch and Chris Morley spoke about Open Babel.

What a great meeting.

It was 50% Open Source Software developers, and 50% pharma industry. Or so I thought at the start. It quickly became apparent that the scientists from pharma were also developing or supporting open source software through a variety of methods. Rajarshi's excellent overview gives a list of some of the talks from industry in this space. I will be following up some of these over the next while.

Of the projects from academia, some which were new to me were Bio-Linux (bio-focused Linux distro available on request as bootable USB sticks from NERC [one of the UK research agencies] - especially useful for teaching), ChemT (GUI for chemical library generation), MOLA (use USB sticks to turn a typical computer lab into a cluster for running AutoDock jobs), and OpenStructure (somewhat similar to PyMol).

The workflow softwares Taverna and KNIME are both doing well. Taverna is widely adopted in the bioinformatics community, while KNIME has considerable mindshare in pharma. An interesting aspect of Taverna is that workflows can be stored at, and users can combine other workflows with full attribution. KNIME now has nodes for RDKit and Indigo (as well as most commercial vendors), toolkits which should be familiar to regular readers here.

Silicos now has several open source offerings for library design and general computer-aided drug design: Sieve (filtering on properties), Pharao (pharmacophore alignment), Piramid (shape-based alignment), Stripper (extract molecular scaffolds according to a variety of schemes), Spectrophores (3D fingerprint for QSAR). An interesting development is the ProfiLib web application which returns a PDF that characterises an uploaded molecular library (in SDF form).

There may be some outcomes from this meeting over the next while, so stay tuned...


Geoff Hutchison said...

Can you find a link to the ChemT project? Sounds interesting, and I wasn't able to make the meeting.

Noel O'Boyle said...

Found it. I've updated the text.

Vincent said...

Hi there :)

As a developper and user of OSS, I'm constantly faced to the plethora of existing OSS licences and their potential incompatibilities..

I heard from participants that lots of people (including some non-industrial OSS developpers) suggested the use of BSD (or such) licences instead of 'classical' (L)GPL licences.

As far as I know, BSD is very permissive... well at least much more than GPL, and I can understand the interest of industrial people for it; but what about OSS developpers ?

Any comments on this topic ?

Cheers :)

Noel O'Boyle said...

Over time, I've become increasingly convinced that scientific software should be released under the BSD.

I will write more on this topic as a blog post, but the essence is that science itself (which we all understand and participate in) is analogous to BSD. We want people to build on our scientific work; in fact, its value is determined by how much it is reused and all the better if people can make money out of it.

The GPL restricts usage (only in certain ways, but restrict it it does). For other software, this may make sense; but not for scientific software.

Noel O'Boyle said...

The usual reason that scientists don't like to choose the BSD is that they want companies to give something back. There is a misconception that somehow the GPL requires companies to contribute modifications to the code back to the original project. They just keep them in-house (or not) either way.